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- EMDB-13765: OMCC C1 at 3.28A - Refinement without symmetry of the outer membr... -

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Basic information

Entry
Database: EMDB / ID: EMD-13765
TitleOMCC C1 at 3.28A - Refinement without symmetry of the outer membrane core complex (O- and I-layer) from the fully-assembled R388 type IV secretion system.
Map dataOMCC C1 at 3.28 - 3D refinement of the Core Complex (OMCC) without symmetry using all particles - Unsharpened
Sample
  • Complex: Type IV secretion system complex
Keywordstype IV secretion system / type 4 secretion system / T4SS / OMCC / core complex / O-layer / I-layer / R388 plasmid / conjugation / bacterial secretion / secretion / secretion system / protein complex / VirB7 / VirB9 / VirB10 / TrwN / TrwF / TrwE / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsMace K / Vadakkepat AK / Waksman G / Lukoyanova N
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
Wellcome Trust217089 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nature / Year: 2022
Title: Cryo-EM structure of a type IV secretion system.
Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong ...Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman /
Abstract: Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
History
DepositionOct 21, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13765.png

Downloads & links

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Map

FileDownload / File: emd_13765.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOMCC C1 at 3.28 - 3D refinement of the Core Complex (OMCC) without symmetry using all particles - Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 320.1 Å		1.07 Å/pix.
x 300 pix.
= 320.1 Å		1.07 Å/pix.
x 300 pix.
= 320.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.24392574 - 0.7559397
Average (Standard dev.)0.012381777 (±0.049714584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 320.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_13765_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Original Ab initio OMCC - Ab initio reconstruction...

Fileemd_13765_additional_1.map
AnnotationOriginal Ab initio OMCC - Ab initio reconstruction without symmetry from 100,000 particles
Projections & Slices
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Additional map: Ab initio model for OMCC C1 - 3D...

Fileemd_13765_additional_2.map
AnnotationAb initio model for OMCC C1 - 3D refinement using original ab initio as initial model, without symmetry from 100,000 particles - Sharpened
Projections & Slices
AxesZYX

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Histogram

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Additional map: Ab initio model for OMCC C1 - 3D...

Fileemd_13765_additional_3.map
AnnotationAb initio model for OMCC C1 - 3D refinement using original ab initio as initial model, without symmetry from 100,000 particles - Unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: OMCC C1 at 3.28 - 3D refinement of...

Fileemd_13765_additional_4.map
AnnotationOMCC C1 at 3.28 - 3D refinement of the Core Complex (OMCC) without symmetry using all particles - Sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: OMCC C1 at 3.28 - Half-A

Fileemd_13765_half_map_1.map
AnnotationOMCC C1 at 3.28 - Half-A
Projections & Slices
AxesZYX

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Half map: OMCC C1 at 3.28 - Half-B

Fileemd_13765_half_map_2.map
AnnotationOMCC C1 at 3.28 - Half-B
Projections & Slices
AxesZYX

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Sample components

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Entire : Type IV secretion system complex

EntireName: Type IV secretion system complex
Components
  • Complex: Type IV secretion system complex

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Supramolecule #1: Type IV secretion system complex

SupramoleculeName: Type IV secretion system complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli) / Strain: R388 plasmid
Molecular weightTheoretical: 2.808 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 349413
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER / Details: Stochastic gradient descent (SGD)

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